Multiple sequence alignment - TraesCS5D01G569400

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G569400 chr5D 100.000 3091 0 0 1 3091 565815527 565818617 0.000000e+00 5709.0
1 TraesCS5D01G569400 chr5D 98.935 2817 28 2 276 3091 260689962 260687147 0.000000e+00 5035.0
2 TraesCS5D01G569400 chr5D 98.367 2817 43 3 276 3091 75136832 75134018 0.000000e+00 4944.0
3 TraesCS5D01G569400 chr7D 98.864 2818 31 1 275 3091 245402432 245399615 0.000000e+00 5025.0
4 TraesCS5D01G569400 chr7D 98.793 2817 31 3 276 3091 54583766 54580952 0.000000e+00 5011.0
5 TraesCS5D01G569400 chr7D 98.545 2817 40 1 276 3091 115100272 115103088 0.000000e+00 4974.0
6 TraesCS5D01G569400 chr6D 98.722 2817 34 2 276 3091 51499464 51502279 0.000000e+00 5001.0
7 TraesCS5D01G569400 chr6D 98.546 2819 34 5 275 3091 472510962 472513775 0.000000e+00 4972.0
8 TraesCS5D01G569400 chr4D 98.438 2817 37 4 276 3091 164897180 164899990 0.000000e+00 4951.0
9 TraesCS5D01G569400 chr1D 98.369 2821 42 4 272 3091 22577399 22574582 0.000000e+00 4951.0
10 TraesCS5D01G569400 chr5B 91.724 145 5 2 141 279 707205480 707205337 8.750000e-46 195.0
11 TraesCS5D01G569400 chr5B 81.395 129 18 4 71 198 707388284 707388161 1.960000e-17 100.0
12 TraesCS5D01G569400 chr5B 95.455 44 1 1 232 274 707388099 707388056 5.530000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G569400 chr5D 565815527 565818617 3090 False 5709 5709 100.000 1 3091 1 chr5D.!!$F1 3090
1 TraesCS5D01G569400 chr5D 260687147 260689962 2815 True 5035 5035 98.935 276 3091 1 chr5D.!!$R2 2815
2 TraesCS5D01G569400 chr5D 75134018 75136832 2814 True 4944 4944 98.367 276 3091 1 chr5D.!!$R1 2815
3 TraesCS5D01G569400 chr7D 245399615 245402432 2817 True 5025 5025 98.864 275 3091 1 chr7D.!!$R2 2816
4 TraesCS5D01G569400 chr7D 54580952 54583766 2814 True 5011 5011 98.793 276 3091 1 chr7D.!!$R1 2815
5 TraesCS5D01G569400 chr7D 115100272 115103088 2816 False 4974 4974 98.545 276 3091 1 chr7D.!!$F1 2815
6 TraesCS5D01G569400 chr6D 51499464 51502279 2815 False 5001 5001 98.722 276 3091 1 chr6D.!!$F1 2815
7 TraesCS5D01G569400 chr6D 472510962 472513775 2813 False 4972 4972 98.546 275 3091 1 chr6D.!!$F2 2816
8 TraesCS5D01G569400 chr4D 164897180 164899990 2810 False 4951 4951 98.438 276 3091 1 chr4D.!!$F1 2815
9 TraesCS5D01G569400 chr1D 22574582 22577399 2817 True 4951 4951 98.369 272 3091 1 chr1D.!!$R1 2819

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
19 20 0.106116 ACCTCTCCTACGATGACCCC 60.106 60.0 0.0 0.0 0.0 4.95 F
63 64 0.107263 TGCTTGCTTGTCACCTGTCA 60.107 50.0 0.0 0.0 0.0 3.58 F
87 88 0.107945 AATGCTCGGCTCCTGAAGTC 60.108 55.0 0.0 0.0 0.0 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1614 1618 1.077716 GGTACATGTCCCACAGCCC 60.078 63.158 0.0 0.0 0.0 5.19 R
1702 1706 5.888105 ACTCAATGCACAGCTTATCATTTC 58.112 37.500 0.0 0.0 0.0 2.17 R
3044 3050 7.880160 ATGAAACCTATGTATTTGCTTGCTA 57.120 32.000 0.0 0.0 0.0 3.49 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 3.516911 ACCTCTCCTACGATGACCC 57.483 57.895 0.00 0.00 0.00 4.46
19 20 0.106116 ACCTCTCCTACGATGACCCC 60.106 60.000 0.00 0.00 0.00 4.95
20 21 1.173444 CCTCTCCTACGATGACCCCG 61.173 65.000 0.00 0.00 0.00 5.73
21 22 0.179026 CTCTCCTACGATGACCCCGA 60.179 60.000 0.00 0.00 0.00 5.14
22 23 0.179026 TCTCCTACGATGACCCCGAG 60.179 60.000 0.00 0.00 0.00 4.63
23 24 0.465824 CTCCTACGATGACCCCGAGT 60.466 60.000 0.00 0.00 0.00 4.18
24 25 0.839277 TCCTACGATGACCCCGAGTA 59.161 55.000 0.00 0.00 0.00 2.59
25 26 1.212688 TCCTACGATGACCCCGAGTAA 59.787 52.381 0.00 0.00 0.00 2.24
26 27 1.336125 CCTACGATGACCCCGAGTAAC 59.664 57.143 0.00 0.00 0.00 2.50
27 28 1.336125 CTACGATGACCCCGAGTAACC 59.664 57.143 0.00 0.00 0.00 2.85
28 29 0.612732 ACGATGACCCCGAGTAACCA 60.613 55.000 0.00 0.00 0.00 3.67
29 30 0.533491 CGATGACCCCGAGTAACCAA 59.467 55.000 0.00 0.00 0.00 3.67
30 31 1.738030 CGATGACCCCGAGTAACCAAC 60.738 57.143 0.00 0.00 0.00 3.77
31 32 1.276989 GATGACCCCGAGTAACCAACA 59.723 52.381 0.00 0.00 0.00 3.33
32 33 1.129917 TGACCCCGAGTAACCAACAA 58.870 50.000 0.00 0.00 0.00 2.83
33 34 1.489649 TGACCCCGAGTAACCAACAAA 59.510 47.619 0.00 0.00 0.00 2.83
34 35 2.106857 TGACCCCGAGTAACCAACAAAT 59.893 45.455 0.00 0.00 0.00 2.32
35 36 3.151554 GACCCCGAGTAACCAACAAATT 58.848 45.455 0.00 0.00 0.00 1.82
36 37 4.202440 TGACCCCGAGTAACCAACAAATTA 60.202 41.667 0.00 0.00 0.00 1.40
37 38 4.329392 ACCCCGAGTAACCAACAAATTAG 58.671 43.478 0.00 0.00 0.00 1.73
38 39 4.202493 ACCCCGAGTAACCAACAAATTAGT 60.202 41.667 0.00 0.00 0.00 2.24
39 40 5.012975 ACCCCGAGTAACCAACAAATTAGTA 59.987 40.000 0.00 0.00 0.00 1.82
40 41 5.352293 CCCCGAGTAACCAACAAATTAGTAC 59.648 44.000 0.00 0.00 0.00 2.73
41 42 5.062558 CCCGAGTAACCAACAAATTAGTACG 59.937 44.000 0.00 0.00 0.00 3.67
42 43 5.445010 CCGAGTAACCAACAAATTAGTACGC 60.445 44.000 0.00 0.00 0.00 4.42
43 44 5.346822 CGAGTAACCAACAAATTAGTACGCT 59.653 40.000 0.00 0.00 0.00 5.07
44 45 6.128742 CGAGTAACCAACAAATTAGTACGCTT 60.129 38.462 0.00 0.00 0.00 4.68
45 46 6.894828 AGTAACCAACAAATTAGTACGCTTG 58.105 36.000 0.00 0.00 0.00 4.01
46 47 4.155310 ACCAACAAATTAGTACGCTTGC 57.845 40.909 0.00 0.00 0.00 4.01
47 48 3.818773 ACCAACAAATTAGTACGCTTGCT 59.181 39.130 0.00 0.00 0.00 3.91
48 49 4.277423 ACCAACAAATTAGTACGCTTGCTT 59.723 37.500 0.00 0.00 0.00 3.91
49 50 4.616802 CCAACAAATTAGTACGCTTGCTTG 59.383 41.667 0.00 0.00 0.00 4.01
50 51 3.821841 ACAAATTAGTACGCTTGCTTGC 58.178 40.909 0.00 0.00 0.00 4.01
51 52 3.502211 ACAAATTAGTACGCTTGCTTGCT 59.498 39.130 0.00 0.00 0.00 3.91
52 53 4.023193 ACAAATTAGTACGCTTGCTTGCTT 60.023 37.500 0.00 0.00 0.00 3.91
53 54 3.747099 ATTAGTACGCTTGCTTGCTTG 57.253 42.857 0.00 0.00 0.00 4.01
54 55 2.163818 TAGTACGCTTGCTTGCTTGT 57.836 45.000 0.00 0.00 0.00 3.16
55 56 0.868406 AGTACGCTTGCTTGCTTGTC 59.132 50.000 0.00 0.00 0.00 3.18
56 57 0.586319 GTACGCTTGCTTGCTTGTCA 59.414 50.000 0.00 0.00 0.00 3.58
57 58 0.586319 TACGCTTGCTTGCTTGTCAC 59.414 50.000 0.00 0.00 0.00 3.67
58 59 1.370900 CGCTTGCTTGCTTGTCACC 60.371 57.895 0.00 0.00 0.00 4.02
59 60 1.789078 CGCTTGCTTGCTTGTCACCT 61.789 55.000 0.00 0.00 0.00 4.00
60 61 0.318445 GCTTGCTTGCTTGTCACCTG 60.318 55.000 0.00 0.00 0.00 4.00
61 62 1.027357 CTTGCTTGCTTGTCACCTGT 58.973 50.000 0.00 0.00 0.00 4.00
62 63 1.002033 CTTGCTTGCTTGTCACCTGTC 60.002 52.381 0.00 0.00 0.00 3.51
63 64 0.107263 TGCTTGCTTGTCACCTGTCA 60.107 50.000 0.00 0.00 0.00 3.58
64 65 0.590195 GCTTGCTTGTCACCTGTCAG 59.410 55.000 0.00 0.00 0.00 3.51
65 66 1.959042 CTTGCTTGTCACCTGTCAGT 58.041 50.000 0.00 0.00 0.00 3.41
66 67 1.600957 CTTGCTTGTCACCTGTCAGTG 59.399 52.381 0.00 0.00 39.20 3.66
67 68 0.541392 TGCTTGTCACCTGTCAGTGT 59.459 50.000 0.00 0.00 38.91 3.55
68 69 1.760029 TGCTTGTCACCTGTCAGTGTA 59.240 47.619 0.00 0.00 38.91 2.90
69 70 2.169561 TGCTTGTCACCTGTCAGTGTAA 59.830 45.455 0.00 0.00 38.91 2.41
70 71 3.181455 TGCTTGTCACCTGTCAGTGTAAT 60.181 43.478 0.00 0.00 38.91 1.89
71 72 3.187227 GCTTGTCACCTGTCAGTGTAATG 59.813 47.826 0.00 0.00 38.91 1.90
72 73 2.766313 TGTCACCTGTCAGTGTAATGC 58.234 47.619 0.00 0.00 38.91 3.56
73 74 2.368548 TGTCACCTGTCAGTGTAATGCT 59.631 45.455 0.00 0.00 38.91 3.79
74 75 2.996621 GTCACCTGTCAGTGTAATGCTC 59.003 50.000 0.00 0.00 38.91 4.26
75 76 1.995484 CACCTGTCAGTGTAATGCTCG 59.005 52.381 0.00 0.00 32.89 5.03
76 77 1.066858 ACCTGTCAGTGTAATGCTCGG 60.067 52.381 0.00 0.00 0.00 4.63
77 78 1.002366 CTGTCAGTGTAATGCTCGGC 58.998 55.000 0.00 0.00 0.00 5.54
78 79 0.608130 TGTCAGTGTAATGCTCGGCT 59.392 50.000 0.00 0.00 0.00 5.52
79 80 1.281899 GTCAGTGTAATGCTCGGCTC 58.718 55.000 0.00 0.00 0.00 4.70
80 81 0.175760 TCAGTGTAATGCTCGGCTCC 59.824 55.000 0.00 0.00 0.00 4.70
81 82 0.176680 CAGTGTAATGCTCGGCTCCT 59.823 55.000 0.00 0.00 0.00 3.69
82 83 0.176680 AGTGTAATGCTCGGCTCCTG 59.823 55.000 0.00 0.00 0.00 3.86
83 84 0.175760 GTGTAATGCTCGGCTCCTGA 59.824 55.000 0.00 0.00 0.00 3.86
84 85 0.901827 TGTAATGCTCGGCTCCTGAA 59.098 50.000 0.00 0.00 0.00 3.02
85 86 1.134699 TGTAATGCTCGGCTCCTGAAG 60.135 52.381 0.00 0.00 0.00 3.02
86 87 1.134670 GTAATGCTCGGCTCCTGAAGT 60.135 52.381 0.00 0.00 0.00 3.01
87 88 0.107945 AATGCTCGGCTCCTGAAGTC 60.108 55.000 0.00 0.00 0.00 3.01
88 89 0.975040 ATGCTCGGCTCCTGAAGTCT 60.975 55.000 0.00 0.00 0.00 3.24
89 90 1.153667 GCTCGGCTCCTGAAGTCTG 60.154 63.158 0.00 0.00 0.00 3.51
90 91 1.882989 GCTCGGCTCCTGAAGTCTGT 61.883 60.000 0.00 0.00 0.00 3.41
91 92 0.172352 CTCGGCTCCTGAAGTCTGTC 59.828 60.000 0.00 0.00 0.00 3.51
92 93 1.153939 CGGCTCCTGAAGTCTGTCG 60.154 63.158 0.00 0.00 0.00 4.35
93 94 1.446966 GGCTCCTGAAGTCTGTCGC 60.447 63.158 0.00 0.00 0.00 5.19
94 95 1.589113 GCTCCTGAAGTCTGTCGCT 59.411 57.895 0.00 0.00 0.00 4.93
95 96 0.457681 GCTCCTGAAGTCTGTCGCTC 60.458 60.000 0.00 0.00 0.00 5.03
96 97 1.173043 CTCCTGAAGTCTGTCGCTCT 58.827 55.000 0.00 0.00 0.00 4.09
97 98 0.884514 TCCTGAAGTCTGTCGCTCTG 59.115 55.000 0.00 0.00 0.00 3.35
98 99 0.600557 CCTGAAGTCTGTCGCTCTGT 59.399 55.000 0.00 0.00 0.00 3.41
99 100 1.813178 CCTGAAGTCTGTCGCTCTGTA 59.187 52.381 0.00 0.00 0.00 2.74
100 101 2.425312 CCTGAAGTCTGTCGCTCTGTAT 59.575 50.000 0.00 0.00 0.00 2.29
101 102 3.433709 CTGAAGTCTGTCGCTCTGTATG 58.566 50.000 0.00 0.00 0.00 2.39
102 103 2.820197 TGAAGTCTGTCGCTCTGTATGT 59.180 45.455 0.00 0.00 0.00 2.29
103 104 4.007659 TGAAGTCTGTCGCTCTGTATGTA 58.992 43.478 0.00 0.00 0.00 2.29
104 105 4.142665 TGAAGTCTGTCGCTCTGTATGTAC 60.143 45.833 0.00 0.00 0.00 2.90
105 106 2.352034 AGTCTGTCGCTCTGTATGTACG 59.648 50.000 0.00 0.00 0.00 3.67
106 107 2.095532 GTCTGTCGCTCTGTATGTACGT 59.904 50.000 0.00 0.00 0.00 3.57
107 108 3.308053 GTCTGTCGCTCTGTATGTACGTA 59.692 47.826 0.00 0.00 0.00 3.57
108 109 3.308053 TCTGTCGCTCTGTATGTACGTAC 59.692 47.826 18.90 18.90 0.00 3.67
109 110 3.002102 TGTCGCTCTGTATGTACGTACA 58.998 45.455 29.15 29.15 40.98 2.90
120 121 8.906636 CTGTATGTACGTACAGTAGAACAAAT 57.093 34.615 33.32 14.06 44.10 2.32
121 122 9.992910 CTGTATGTACGTACAGTAGAACAAATA 57.007 33.333 33.32 13.13 44.10 1.40
122 123 9.773328 TGTATGTACGTACAGTAGAACAAATAC 57.227 33.333 30.15 22.24 39.92 1.89
123 124 9.226345 GTATGTACGTACAGTAGAACAAATACC 57.774 37.037 30.15 7.99 39.92 2.73
124 125 7.213216 TGTACGTACAGTAGAACAAATACCA 57.787 36.000 24.10 0.00 35.72 3.25
125 126 7.307694 TGTACGTACAGTAGAACAAATACCAG 58.692 38.462 24.10 0.00 35.72 4.00
126 127 6.336842 ACGTACAGTAGAACAAATACCAGT 57.663 37.500 0.00 0.00 0.00 4.00
127 128 6.385033 ACGTACAGTAGAACAAATACCAGTC 58.615 40.000 0.00 0.00 0.00 3.51
128 129 6.208204 ACGTACAGTAGAACAAATACCAGTCT 59.792 38.462 0.00 0.00 0.00 3.24
129 130 7.088905 CGTACAGTAGAACAAATACCAGTCTT 58.911 38.462 0.00 0.00 0.00 3.01
130 131 8.239314 CGTACAGTAGAACAAATACCAGTCTTA 58.761 37.037 0.00 0.00 0.00 2.10
131 132 9.570488 GTACAGTAGAACAAATACCAGTCTTAG 57.430 37.037 0.00 0.00 0.00 2.18
132 133 8.191534 ACAGTAGAACAAATACCAGTCTTAGT 57.808 34.615 0.00 0.00 0.00 2.24
133 134 8.088981 ACAGTAGAACAAATACCAGTCTTAGTG 58.911 37.037 0.00 0.00 0.00 2.74
134 135 8.088981 CAGTAGAACAAATACCAGTCTTAGTGT 58.911 37.037 0.00 0.00 0.00 3.55
135 136 8.088981 AGTAGAACAAATACCAGTCTTAGTGTG 58.911 37.037 0.00 0.00 0.00 3.82
136 137 7.062749 AGAACAAATACCAGTCTTAGTGTGA 57.937 36.000 0.00 0.00 0.00 3.58
137 138 7.506114 AGAACAAATACCAGTCTTAGTGTGAA 58.494 34.615 0.00 0.00 0.00 3.18
138 139 7.657761 AGAACAAATACCAGTCTTAGTGTGAAG 59.342 37.037 0.00 0.00 0.00 3.02
139 140 7.062749 ACAAATACCAGTCTTAGTGTGAAGA 57.937 36.000 0.00 0.00 32.97 2.87
140 141 7.506114 ACAAATACCAGTCTTAGTGTGAAGAA 58.494 34.615 0.00 0.00 37.20 2.52
141 142 7.990886 ACAAATACCAGTCTTAGTGTGAAGAAA 59.009 33.333 0.00 0.00 37.20 2.52
142 143 9.003658 CAAATACCAGTCTTAGTGTGAAGAAAT 57.996 33.333 0.00 0.00 37.20 2.17
143 144 8.553459 AATACCAGTCTTAGTGTGAAGAAATG 57.447 34.615 0.00 0.00 37.20 2.32
144 145 6.174720 ACCAGTCTTAGTGTGAAGAAATGA 57.825 37.500 0.00 0.00 37.20 2.57
145 146 6.591935 ACCAGTCTTAGTGTGAAGAAATGAA 58.408 36.000 0.00 0.00 37.20 2.57
146 147 6.708054 ACCAGTCTTAGTGTGAAGAAATGAAG 59.292 38.462 0.00 0.00 37.20 3.02
147 148 6.348050 CCAGTCTTAGTGTGAAGAAATGAAGC 60.348 42.308 0.00 0.00 37.20 3.86
148 149 6.203530 CAGTCTTAGTGTGAAGAAATGAAGCA 59.796 38.462 0.00 0.00 37.20 3.91
149 150 6.426328 AGTCTTAGTGTGAAGAAATGAAGCAG 59.574 38.462 0.00 0.00 37.20 4.24
150 151 6.203723 GTCTTAGTGTGAAGAAATGAAGCAGT 59.796 38.462 0.00 0.00 37.20 4.40
151 152 6.425114 TCTTAGTGTGAAGAAATGAAGCAGTC 59.575 38.462 0.00 0.00 32.46 3.51
152 153 3.817647 AGTGTGAAGAAATGAAGCAGTCC 59.182 43.478 0.00 0.00 0.00 3.85
153 154 3.565482 GTGTGAAGAAATGAAGCAGTCCA 59.435 43.478 0.00 0.00 0.00 4.02
154 155 4.036734 GTGTGAAGAAATGAAGCAGTCCAA 59.963 41.667 0.00 0.00 0.00 3.53
155 156 4.828939 TGTGAAGAAATGAAGCAGTCCAAT 59.171 37.500 0.00 0.00 0.00 3.16
156 157 5.048504 TGTGAAGAAATGAAGCAGTCCAATC 60.049 40.000 0.00 0.00 0.00 2.67
157 158 4.154737 TGAAGAAATGAAGCAGTCCAATCG 59.845 41.667 0.00 0.00 0.00 3.34
158 159 2.421424 AGAAATGAAGCAGTCCAATCGC 59.579 45.455 0.00 0.00 0.00 4.58
159 160 2.119801 AATGAAGCAGTCCAATCGCT 57.880 45.000 0.00 0.00 37.68 4.93
160 161 2.988010 ATGAAGCAGTCCAATCGCTA 57.012 45.000 0.00 0.00 34.11 4.26
161 162 2.988010 TGAAGCAGTCCAATCGCTAT 57.012 45.000 0.00 0.00 34.11 2.97
162 163 3.266510 TGAAGCAGTCCAATCGCTATT 57.733 42.857 0.00 0.00 34.11 1.73
163 164 3.198068 TGAAGCAGTCCAATCGCTATTC 58.802 45.455 0.00 0.00 34.11 1.75
164 165 2.988010 AGCAGTCCAATCGCTATTCA 57.012 45.000 0.00 0.00 33.25 2.57
165 166 3.482156 AGCAGTCCAATCGCTATTCAT 57.518 42.857 0.00 0.00 33.25 2.57
166 167 3.397482 AGCAGTCCAATCGCTATTCATC 58.603 45.455 0.00 0.00 33.25 2.92
167 168 3.070734 AGCAGTCCAATCGCTATTCATCT 59.929 43.478 0.00 0.00 33.25 2.90
168 169 3.186001 GCAGTCCAATCGCTATTCATCTG 59.814 47.826 0.00 0.00 0.00 2.90
169 170 3.744942 CAGTCCAATCGCTATTCATCTGG 59.255 47.826 0.00 0.00 0.00 3.86
170 171 3.643320 AGTCCAATCGCTATTCATCTGGA 59.357 43.478 0.00 0.00 0.00 3.86
171 172 4.101585 AGTCCAATCGCTATTCATCTGGAA 59.898 41.667 0.00 0.00 40.46 3.53
173 174 5.471456 GTCCAATCGCTATTCATCTGGAATT 59.529 40.000 0.00 0.00 43.76 2.17
174 175 5.471116 TCCAATCGCTATTCATCTGGAATTG 59.529 40.000 0.00 0.00 43.76 2.32
175 176 5.240183 CCAATCGCTATTCATCTGGAATTGT 59.760 40.000 0.00 0.00 43.76 2.71
176 177 6.369005 CAATCGCTATTCATCTGGAATTGTC 58.631 40.000 0.00 0.00 43.76 3.18
177 178 5.282055 TCGCTATTCATCTGGAATTGTCT 57.718 39.130 0.00 0.00 43.76 3.41
178 179 5.292765 TCGCTATTCATCTGGAATTGTCTC 58.707 41.667 0.00 0.00 43.76 3.36
179 180 5.052481 CGCTATTCATCTGGAATTGTCTCA 58.948 41.667 0.00 0.00 43.76 3.27
180 181 5.525012 CGCTATTCATCTGGAATTGTCTCAA 59.475 40.000 0.00 0.00 43.76 3.02
181 182 6.292757 CGCTATTCATCTGGAATTGTCTCAAG 60.293 42.308 0.00 0.00 43.76 3.02
182 183 6.765036 GCTATTCATCTGGAATTGTCTCAAGA 59.235 38.462 0.00 0.00 43.76 3.02
183 184 7.281774 GCTATTCATCTGGAATTGTCTCAAGAA 59.718 37.037 0.00 0.00 43.76 2.52
184 185 9.170734 CTATTCATCTGGAATTGTCTCAAGAAA 57.829 33.333 0.00 0.00 43.76 2.52
185 186 8.591114 ATTCATCTGGAATTGTCTCAAGAAAT 57.409 30.769 0.00 0.00 43.76 2.17
186 187 8.413309 TTCATCTGGAATTGTCTCAAGAAATT 57.587 30.769 0.00 0.00 0.00 1.82
187 188 9.519191 TTCATCTGGAATTGTCTCAAGAAATTA 57.481 29.630 0.00 0.00 0.00 1.40
188 189 9.519191 TCATCTGGAATTGTCTCAAGAAATTAA 57.481 29.630 0.00 0.00 0.00 1.40
189 190 9.784680 CATCTGGAATTGTCTCAAGAAATTAAG 57.215 33.333 0.00 0.00 0.00 1.85
190 191 7.820648 TCTGGAATTGTCTCAAGAAATTAAGC 58.179 34.615 0.00 0.00 0.00 3.09
191 192 7.448161 TCTGGAATTGTCTCAAGAAATTAAGCA 59.552 33.333 0.00 0.00 0.00 3.91
192 193 7.596494 TGGAATTGTCTCAAGAAATTAAGCAG 58.404 34.615 0.00 0.00 0.00 4.24
193 194 7.448161 TGGAATTGTCTCAAGAAATTAAGCAGA 59.552 33.333 0.00 0.00 0.00 4.26
194 195 7.752686 GGAATTGTCTCAAGAAATTAAGCAGAC 59.247 37.037 0.00 0.00 0.00 3.51
195 196 6.560253 TTGTCTCAAGAAATTAAGCAGACC 57.440 37.500 0.00 0.00 0.00 3.85
196 197 5.620206 TGTCTCAAGAAATTAAGCAGACCA 58.380 37.500 0.00 0.00 0.00 4.02
197 198 5.702670 TGTCTCAAGAAATTAAGCAGACCAG 59.297 40.000 0.00 0.00 0.00 4.00
198 199 5.934625 GTCTCAAGAAATTAAGCAGACCAGA 59.065 40.000 0.00 0.00 0.00 3.86
199 200 6.428159 GTCTCAAGAAATTAAGCAGACCAGAA 59.572 38.462 0.00 0.00 0.00 3.02
200 201 6.652481 TCTCAAGAAATTAAGCAGACCAGAAG 59.348 38.462 0.00 0.00 0.00 2.85
201 202 6.533730 TCAAGAAATTAAGCAGACCAGAAGA 58.466 36.000 0.00 0.00 0.00 2.87
202 203 6.998074 TCAAGAAATTAAGCAGACCAGAAGAA 59.002 34.615 0.00 0.00 0.00 2.52
203 204 7.667219 TCAAGAAATTAAGCAGACCAGAAGAAT 59.333 33.333 0.00 0.00 0.00 2.40
204 205 8.950210 CAAGAAATTAAGCAGACCAGAAGAATA 58.050 33.333 0.00 0.00 0.00 1.75
205 206 9.520515 AAGAAATTAAGCAGACCAGAAGAATAA 57.479 29.630 0.00 0.00 0.00 1.40
206 207 9.171877 AGAAATTAAGCAGACCAGAAGAATAAG 57.828 33.333 0.00 0.00 0.00 1.73
207 208 8.870075 AAATTAAGCAGACCAGAAGAATAAGT 57.130 30.769 0.00 0.00 0.00 2.24
208 209 9.959721 AAATTAAGCAGACCAGAAGAATAAGTA 57.040 29.630 0.00 0.00 0.00 2.24
209 210 9.959721 AATTAAGCAGACCAGAAGAATAAGTAA 57.040 29.630 0.00 0.00 0.00 2.24
211 212 9.601217 TTAAGCAGACCAGAAGAATAAGTAATC 57.399 33.333 0.00 0.00 0.00 1.75
212 213 7.430760 AGCAGACCAGAAGAATAAGTAATCT 57.569 36.000 0.00 0.00 0.00 2.40
213 214 7.496747 AGCAGACCAGAAGAATAAGTAATCTC 58.503 38.462 0.00 0.00 0.00 2.75
214 215 6.419413 GCAGACCAGAAGAATAAGTAATCTCG 59.581 42.308 0.00 0.00 0.00 4.04
215 216 6.419413 CAGACCAGAAGAATAAGTAATCTCGC 59.581 42.308 0.00 0.00 0.00 5.03
216 217 6.096987 AGACCAGAAGAATAAGTAATCTCGCA 59.903 38.462 0.00 0.00 0.00 5.10
217 218 6.043411 ACCAGAAGAATAAGTAATCTCGCAC 58.957 40.000 0.00 0.00 0.00 5.34
218 219 6.042777 CCAGAAGAATAAGTAATCTCGCACA 58.957 40.000 0.00 0.00 0.00 4.57
219 220 6.535150 CCAGAAGAATAAGTAATCTCGCACAA 59.465 38.462 0.00 0.00 0.00 3.33
220 221 7.064609 CCAGAAGAATAAGTAATCTCGCACAAA 59.935 37.037 0.00 0.00 0.00 2.83
221 222 7.900352 CAGAAGAATAAGTAATCTCGCACAAAC 59.100 37.037 0.00 0.00 0.00 2.93
222 223 7.819900 AGAAGAATAAGTAATCTCGCACAAACT 59.180 33.333 0.00 0.00 0.00 2.66
223 224 7.907214 AGAATAAGTAATCTCGCACAAACTT 57.093 32.000 0.00 0.00 0.00 2.66
224 225 8.997621 AGAATAAGTAATCTCGCACAAACTTA 57.002 30.769 0.00 0.00 34.84 2.24
225 226 9.431887 AGAATAAGTAATCTCGCACAAACTTAA 57.568 29.630 0.00 0.00 34.25 1.85
229 230 7.907214 AGTAATCTCGCACAAACTTAATTCT 57.093 32.000 0.00 0.00 0.00 2.40
230 231 7.743104 AGTAATCTCGCACAAACTTAATTCTG 58.257 34.615 0.00 0.00 0.00 3.02
231 232 5.551760 ATCTCGCACAAACTTAATTCTGG 57.448 39.130 0.00 0.00 0.00 3.86
232 233 3.188460 TCTCGCACAAACTTAATTCTGGC 59.812 43.478 0.00 0.00 0.00 4.85
233 234 2.881513 TCGCACAAACTTAATTCTGGCA 59.118 40.909 0.00 0.00 0.00 4.92
234 235 3.505680 TCGCACAAACTTAATTCTGGCAT 59.494 39.130 0.00 0.00 0.00 4.40
235 236 4.022416 TCGCACAAACTTAATTCTGGCATT 60.022 37.500 0.00 0.00 0.00 3.56
236 237 4.685628 CGCACAAACTTAATTCTGGCATTT 59.314 37.500 0.00 0.00 0.00 2.32
237 238 5.164061 CGCACAAACTTAATTCTGGCATTTC 60.164 40.000 0.00 0.00 0.00 2.17
238 239 5.695816 GCACAAACTTAATTCTGGCATTTCA 59.304 36.000 0.00 0.00 0.00 2.69
239 240 6.128742 GCACAAACTTAATTCTGGCATTTCAG 60.129 38.462 0.00 0.00 36.17 3.02
240 241 6.925165 CACAAACTTAATTCTGGCATTTCAGT 59.075 34.615 0.00 0.00 36.25 3.41
241 242 8.081633 CACAAACTTAATTCTGGCATTTCAGTA 58.918 33.333 0.00 0.00 36.25 2.74
242 243 8.637986 ACAAACTTAATTCTGGCATTTCAGTAA 58.362 29.630 0.00 0.00 36.25 2.24
243 244 9.474920 CAAACTTAATTCTGGCATTTCAGTAAA 57.525 29.630 0.00 0.00 36.25 2.01
249 250 8.707938 AATTCTGGCATTTCAGTAAAATTAGC 57.292 30.769 0.00 0.00 35.32 3.09
250 251 7.466746 TTCTGGCATTTCAGTAAAATTAGCT 57.533 32.000 0.00 0.00 35.32 3.32
251 252 7.466746 TCTGGCATTTCAGTAAAATTAGCTT 57.533 32.000 0.00 0.00 35.32 3.74
252 253 7.315142 TCTGGCATTTCAGTAAAATTAGCTTG 58.685 34.615 0.00 0.00 35.32 4.01
253 254 5.868801 TGGCATTTCAGTAAAATTAGCTTGC 59.131 36.000 0.00 0.00 35.32 4.01
254 255 5.291858 GGCATTTCAGTAAAATTAGCTTGCC 59.708 40.000 0.00 0.00 37.98 4.52
255 256 6.101997 GCATTTCAGTAAAATTAGCTTGCCT 58.898 36.000 0.00 0.00 35.32 4.75
256 257 6.035327 GCATTTCAGTAAAATTAGCTTGCCTG 59.965 38.462 0.00 0.00 35.32 4.85
257 258 6.892658 TTTCAGTAAAATTAGCTTGCCTGA 57.107 33.333 0.00 0.00 0.00 3.86
258 259 6.892658 TTCAGTAAAATTAGCTTGCCTGAA 57.107 33.333 0.00 0.00 0.00 3.02
259 260 6.254281 TCAGTAAAATTAGCTTGCCTGAAC 57.746 37.500 0.00 0.00 0.00 3.18
260 261 5.767665 TCAGTAAAATTAGCTTGCCTGAACA 59.232 36.000 0.00 0.00 0.00 3.18
261 262 6.264292 TCAGTAAAATTAGCTTGCCTGAACAA 59.736 34.615 0.00 0.00 0.00 2.83
270 271 3.957468 CTTGCCTGAACAAGTCTGAAAC 58.043 45.455 0.00 0.00 41.74 2.78
454 455 2.737180 CTGTCAGGCCACGTCAGT 59.263 61.111 5.01 0.00 0.00 3.41
975 977 5.019470 TGATCTATGTCTGGTTCTGTGAGT 58.981 41.667 0.00 0.00 0.00 3.41
1051 1053 0.473755 TCTTTTCTGTGGCCAGCTGA 59.526 50.000 17.39 8.26 38.66 4.26
1118 1120 3.030291 AGTGTGTGGCATTTGAAGGAAA 58.970 40.909 0.00 0.00 0.00 3.13
1614 1618 4.691860 ATTCTTCAGAATTGCTTGTCCG 57.308 40.909 0.00 0.00 41.64 4.79
1702 1706 1.909700 TTGGCCAAGCTTAAGACTGG 58.090 50.000 16.05 15.58 0.00 4.00
1709 1713 4.400567 GCCAAGCTTAAGACTGGAAATGAT 59.599 41.667 21.46 0.00 0.00 2.45
3076 3082 9.480053 GCAAATACATAGGTTTCATAAATGCAT 57.520 29.630 0.00 0.00 0.00 3.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.106116 GGGGTCATCGTAGGAGAGGT 60.106 60.000 0.00 0.00 0.00 3.85
1 2 1.173444 CGGGGTCATCGTAGGAGAGG 61.173 65.000 0.00 0.00 0.00 3.69
2 3 0.179026 TCGGGGTCATCGTAGGAGAG 60.179 60.000 0.00 0.00 0.00 3.20
3 4 0.179026 CTCGGGGTCATCGTAGGAGA 60.179 60.000 0.00 0.00 0.00 3.71
4 5 0.465824 ACTCGGGGTCATCGTAGGAG 60.466 60.000 0.00 0.00 0.00 3.69
5 6 0.839277 TACTCGGGGTCATCGTAGGA 59.161 55.000 0.00 0.00 0.00 2.94
6 7 1.336125 GTTACTCGGGGTCATCGTAGG 59.664 57.143 0.00 0.00 0.00 3.18
7 8 1.336125 GGTTACTCGGGGTCATCGTAG 59.664 57.143 0.00 0.00 0.00 3.51
8 9 1.340893 TGGTTACTCGGGGTCATCGTA 60.341 52.381 0.00 0.00 0.00 3.43
9 10 0.612732 TGGTTACTCGGGGTCATCGT 60.613 55.000 0.00 0.00 0.00 3.73
10 11 0.533491 TTGGTTACTCGGGGTCATCG 59.467 55.000 0.00 0.00 0.00 3.84
11 12 1.276989 TGTTGGTTACTCGGGGTCATC 59.723 52.381 0.00 0.00 0.00 2.92
12 13 1.354101 TGTTGGTTACTCGGGGTCAT 58.646 50.000 0.00 0.00 0.00 3.06
13 14 1.129917 TTGTTGGTTACTCGGGGTCA 58.870 50.000 0.00 0.00 0.00 4.02
14 15 2.259266 TTTGTTGGTTACTCGGGGTC 57.741 50.000 0.00 0.00 0.00 4.46
15 16 2.963599 ATTTGTTGGTTACTCGGGGT 57.036 45.000 0.00 0.00 0.00 4.95
16 17 4.329392 ACTAATTTGTTGGTTACTCGGGG 58.671 43.478 0.00 0.00 0.00 5.73
17 18 5.062558 CGTACTAATTTGTTGGTTACTCGGG 59.937 44.000 0.00 0.00 0.00 5.14
18 19 5.445010 GCGTACTAATTTGTTGGTTACTCGG 60.445 44.000 0.00 0.00 0.00 4.63
19 20 5.346822 AGCGTACTAATTTGTTGGTTACTCG 59.653 40.000 0.00 0.00 0.00 4.18
20 21 6.716898 AGCGTACTAATTTGTTGGTTACTC 57.283 37.500 0.00 0.00 0.00 2.59
21 22 6.567132 GCAAGCGTACTAATTTGTTGGTTACT 60.567 38.462 0.00 0.00 0.00 2.24
22 23 5.566395 GCAAGCGTACTAATTTGTTGGTTAC 59.434 40.000 0.00 0.00 0.00 2.50
23 24 5.470777 AGCAAGCGTACTAATTTGTTGGTTA 59.529 36.000 0.00 0.00 0.00 2.85
24 25 4.277423 AGCAAGCGTACTAATTTGTTGGTT 59.723 37.500 0.00 1.36 0.00 3.67
25 26 3.818773 AGCAAGCGTACTAATTTGTTGGT 59.181 39.130 0.00 0.00 0.00 3.67
26 27 4.419522 AGCAAGCGTACTAATTTGTTGG 57.580 40.909 0.00 0.00 0.00 3.77
27 28 4.088496 GCAAGCAAGCGTACTAATTTGTTG 59.912 41.667 0.00 0.00 0.00 3.33
28 29 4.023193 AGCAAGCAAGCGTACTAATTTGTT 60.023 37.500 0.00 0.00 40.15 2.83
29 30 3.502211 AGCAAGCAAGCGTACTAATTTGT 59.498 39.130 0.00 0.00 40.15 2.83
30 31 4.083581 AGCAAGCAAGCGTACTAATTTG 57.916 40.909 0.00 0.00 40.15 2.32
31 32 4.023193 ACAAGCAAGCAAGCGTACTAATTT 60.023 37.500 0.00 0.00 40.15 1.82
32 33 3.502211 ACAAGCAAGCAAGCGTACTAATT 59.498 39.130 0.00 0.00 40.15 1.40
33 34 3.074412 ACAAGCAAGCAAGCGTACTAAT 58.926 40.909 0.00 0.00 40.15 1.73
34 35 2.478894 GACAAGCAAGCAAGCGTACTAA 59.521 45.455 0.00 0.00 40.15 2.24
35 36 2.066262 GACAAGCAAGCAAGCGTACTA 58.934 47.619 0.00 0.00 40.15 1.82
36 37 0.868406 GACAAGCAAGCAAGCGTACT 59.132 50.000 0.00 0.00 40.15 2.73
37 38 0.586319 TGACAAGCAAGCAAGCGTAC 59.414 50.000 0.00 0.00 40.15 3.67
38 39 0.586319 GTGACAAGCAAGCAAGCGTA 59.414 50.000 0.00 0.00 40.15 4.42
39 40 1.356624 GTGACAAGCAAGCAAGCGT 59.643 52.632 0.00 0.00 40.15 5.07
40 41 1.370900 GGTGACAAGCAAGCAAGCG 60.371 57.895 0.00 0.00 40.15 4.68
41 42 0.318445 CAGGTGACAAGCAAGCAAGC 60.318 55.000 0.00 0.00 0.00 4.01
42 43 1.002033 GACAGGTGACAAGCAAGCAAG 60.002 52.381 0.00 0.00 0.00 4.01
43 44 1.024271 GACAGGTGACAAGCAAGCAA 58.976 50.000 0.00 0.00 0.00 3.91
44 45 0.107263 TGACAGGTGACAAGCAAGCA 60.107 50.000 0.00 0.00 0.00 3.91
45 46 0.590195 CTGACAGGTGACAAGCAAGC 59.410 55.000 0.00 0.00 0.00 4.01
46 47 1.600957 CACTGACAGGTGACAAGCAAG 59.399 52.381 7.51 0.00 39.34 4.01
47 48 1.065491 ACACTGACAGGTGACAAGCAA 60.065 47.619 7.51 0.00 40.13 3.91
48 49 0.541392 ACACTGACAGGTGACAAGCA 59.459 50.000 7.51 0.00 40.13 3.91
49 50 2.526304 TACACTGACAGGTGACAAGC 57.474 50.000 7.51 0.00 40.13 4.01
50 51 3.187227 GCATTACACTGACAGGTGACAAG 59.813 47.826 7.51 0.00 40.13 3.16
51 52 3.138304 GCATTACACTGACAGGTGACAA 58.862 45.455 7.51 4.08 40.13 3.18
52 53 2.368548 AGCATTACACTGACAGGTGACA 59.631 45.455 7.51 0.00 40.13 3.58
53 54 2.996621 GAGCATTACACTGACAGGTGAC 59.003 50.000 7.51 0.00 40.13 3.67
54 55 2.352715 CGAGCATTACACTGACAGGTGA 60.353 50.000 7.51 0.00 40.13 4.02
55 56 1.995484 CGAGCATTACACTGACAGGTG 59.005 52.381 7.51 5.54 42.34 4.00
56 57 1.066858 CCGAGCATTACACTGACAGGT 60.067 52.381 7.51 4.73 0.00 4.00
57 58 1.645034 CCGAGCATTACACTGACAGG 58.355 55.000 7.51 0.00 0.00 4.00
58 59 1.002366 GCCGAGCATTACACTGACAG 58.998 55.000 0.00 0.00 0.00 3.51
59 60 0.608130 AGCCGAGCATTACACTGACA 59.392 50.000 0.00 0.00 0.00 3.58
60 61 1.281899 GAGCCGAGCATTACACTGAC 58.718 55.000 0.00 0.00 0.00 3.51
61 62 0.175760 GGAGCCGAGCATTACACTGA 59.824 55.000 0.00 0.00 0.00 3.41
62 63 0.176680 AGGAGCCGAGCATTACACTG 59.823 55.000 0.00 0.00 0.00 3.66
63 64 0.176680 CAGGAGCCGAGCATTACACT 59.823 55.000 0.00 0.00 0.00 3.55
64 65 0.175760 TCAGGAGCCGAGCATTACAC 59.824 55.000 0.00 0.00 0.00 2.90
65 66 0.901827 TTCAGGAGCCGAGCATTACA 59.098 50.000 0.00 0.00 0.00 2.41
66 67 1.134670 ACTTCAGGAGCCGAGCATTAC 60.135 52.381 0.00 0.00 0.00 1.89
67 68 1.137086 GACTTCAGGAGCCGAGCATTA 59.863 52.381 0.00 0.00 0.00 1.90
68 69 0.107945 GACTTCAGGAGCCGAGCATT 60.108 55.000 0.00 0.00 0.00 3.56
69 70 0.975040 AGACTTCAGGAGCCGAGCAT 60.975 55.000 0.00 0.00 0.00 3.79
70 71 1.607756 AGACTTCAGGAGCCGAGCA 60.608 57.895 0.00 0.00 0.00 4.26
71 72 1.153667 CAGACTTCAGGAGCCGAGC 60.154 63.158 0.00 0.00 0.00 5.03
72 73 0.172352 GACAGACTTCAGGAGCCGAG 59.828 60.000 0.00 0.00 0.00 4.63
73 74 1.587043 CGACAGACTTCAGGAGCCGA 61.587 60.000 0.00 0.00 0.00 5.54
74 75 1.153939 CGACAGACTTCAGGAGCCG 60.154 63.158 0.00 0.00 0.00 5.52
75 76 1.446966 GCGACAGACTTCAGGAGCC 60.447 63.158 0.00 0.00 0.00 4.70
76 77 0.457681 GAGCGACAGACTTCAGGAGC 60.458 60.000 0.00 0.00 0.00 4.70
77 78 1.135431 CAGAGCGACAGACTTCAGGAG 60.135 57.143 0.00 0.00 0.00 3.69
78 79 0.884514 CAGAGCGACAGACTTCAGGA 59.115 55.000 0.00 0.00 0.00 3.86
79 80 0.600557 ACAGAGCGACAGACTTCAGG 59.399 55.000 0.00 0.00 0.00 3.86
80 81 3.119673 ACATACAGAGCGACAGACTTCAG 60.120 47.826 0.00 0.00 0.00 3.02
81 82 2.820197 ACATACAGAGCGACAGACTTCA 59.180 45.455 0.00 0.00 0.00 3.02
82 83 3.495670 ACATACAGAGCGACAGACTTC 57.504 47.619 0.00 0.00 0.00 3.01
83 84 3.181509 CGTACATACAGAGCGACAGACTT 60.182 47.826 0.00 0.00 0.00 3.01
84 85 2.352034 CGTACATACAGAGCGACAGACT 59.648 50.000 0.00 0.00 0.00 3.24
85 86 2.095532 ACGTACATACAGAGCGACAGAC 59.904 50.000 0.00 0.00 0.00 3.51
86 87 2.353323 ACGTACATACAGAGCGACAGA 58.647 47.619 0.00 0.00 0.00 3.41
87 88 2.826979 ACGTACATACAGAGCGACAG 57.173 50.000 0.00 0.00 0.00 3.51
88 89 3.002102 TGTACGTACATACAGAGCGACA 58.998 45.455 24.10 0.00 31.38 4.35
89 90 3.663464 TGTACGTACATACAGAGCGAC 57.337 47.619 24.10 0.00 31.38 5.19
96 97 9.773328 GTATTTGTTCTACTGTACGTACATACA 57.227 33.333 27.50 20.86 35.36 2.29
97 98 9.226345 GGTATTTGTTCTACTGTACGTACATAC 57.774 37.037 27.50 20.33 35.36 2.39
98 99 8.955388 TGGTATTTGTTCTACTGTACGTACATA 58.045 33.333 27.50 19.14 35.36 2.29
99 100 7.829725 TGGTATTTGTTCTACTGTACGTACAT 58.170 34.615 27.50 19.05 35.36 2.29
100 101 7.040478 ACTGGTATTTGTTCTACTGTACGTACA 60.040 37.037 25.88 25.88 34.56 2.90
101 102 7.308435 ACTGGTATTTGTTCTACTGTACGTAC 58.692 38.462 18.90 18.90 0.00 3.67
102 103 7.391554 AGACTGGTATTTGTTCTACTGTACGTA 59.608 37.037 0.00 0.00 0.00 3.57
103 104 6.208204 AGACTGGTATTTGTTCTACTGTACGT 59.792 38.462 0.00 0.00 0.00 3.57
104 105 6.618811 AGACTGGTATTTGTTCTACTGTACG 58.381 40.000 0.00 0.00 0.00 3.67
105 106 9.570488 CTAAGACTGGTATTTGTTCTACTGTAC 57.430 37.037 0.00 0.00 0.00 2.90
106 107 9.305555 ACTAAGACTGGTATTTGTTCTACTGTA 57.694 33.333 0.00 0.00 0.00 2.74
107 108 8.088981 CACTAAGACTGGTATTTGTTCTACTGT 58.911 37.037 0.00 0.00 0.00 3.55
108 109 8.088981 ACACTAAGACTGGTATTTGTTCTACTG 58.911 37.037 0.00 0.00 0.00 2.74
109 110 8.088981 CACACTAAGACTGGTATTTGTTCTACT 58.911 37.037 0.00 0.00 0.00 2.57
110 111 8.086522 TCACACTAAGACTGGTATTTGTTCTAC 58.913 37.037 0.00 0.00 0.00 2.59
111 112 8.185506 TCACACTAAGACTGGTATTTGTTCTA 57.814 34.615 0.00 0.00 0.00 2.10
112 113 7.062749 TCACACTAAGACTGGTATTTGTTCT 57.937 36.000 0.00 0.00 0.00 3.01
113 114 7.656137 TCTTCACACTAAGACTGGTATTTGTTC 59.344 37.037 0.00 0.00 30.54 3.18
114 115 7.506114 TCTTCACACTAAGACTGGTATTTGTT 58.494 34.615 0.00 0.00 30.54 2.83
115 116 7.062749 TCTTCACACTAAGACTGGTATTTGT 57.937 36.000 0.00 0.00 30.54 2.83
116 117 7.962964 TTCTTCACACTAAGACTGGTATTTG 57.037 36.000 0.00 0.00 35.25 2.32
117 118 9.003658 CATTTCTTCACACTAAGACTGGTATTT 57.996 33.333 0.00 0.00 35.25 1.40
118 119 8.375506 TCATTTCTTCACACTAAGACTGGTATT 58.624 33.333 0.00 0.00 35.25 1.89
119 120 7.907389 TCATTTCTTCACACTAAGACTGGTAT 58.093 34.615 0.00 0.00 35.25 2.73
120 121 7.297936 TCATTTCTTCACACTAAGACTGGTA 57.702 36.000 0.00 0.00 35.25 3.25
121 122 6.174720 TCATTTCTTCACACTAAGACTGGT 57.825 37.500 0.00 0.00 35.25 4.00
122 123 6.348050 GCTTCATTTCTTCACACTAAGACTGG 60.348 42.308 0.00 0.00 35.25 4.00
123 124 6.203530 TGCTTCATTTCTTCACACTAAGACTG 59.796 38.462 0.00 0.00 35.25 3.51
124 125 6.291377 TGCTTCATTTCTTCACACTAAGACT 58.709 36.000 0.00 0.00 35.25 3.24
125 126 6.203723 ACTGCTTCATTTCTTCACACTAAGAC 59.796 38.462 0.00 0.00 35.25 3.01
126 127 6.291377 ACTGCTTCATTTCTTCACACTAAGA 58.709 36.000 0.00 0.00 33.69 2.10
127 128 6.348050 GGACTGCTTCATTTCTTCACACTAAG 60.348 42.308 0.00 0.00 0.00 2.18
128 129 5.470098 GGACTGCTTCATTTCTTCACACTAA 59.530 40.000 0.00 0.00 0.00 2.24
129 130 4.997395 GGACTGCTTCATTTCTTCACACTA 59.003 41.667 0.00 0.00 0.00 2.74
130 131 3.817647 GGACTGCTTCATTTCTTCACACT 59.182 43.478 0.00 0.00 0.00 3.55
131 132 3.565482 TGGACTGCTTCATTTCTTCACAC 59.435 43.478 0.00 0.00 0.00 3.82
132 133 3.819368 TGGACTGCTTCATTTCTTCACA 58.181 40.909 0.00 0.00 0.00 3.58
133 134 4.836125 TTGGACTGCTTCATTTCTTCAC 57.164 40.909 0.00 0.00 0.00 3.18
134 135 4.154737 CGATTGGACTGCTTCATTTCTTCA 59.845 41.667 0.00 0.00 0.00 3.02
135 136 4.656041 CGATTGGACTGCTTCATTTCTTC 58.344 43.478 0.00 0.00 0.00 2.87
136 137 3.119708 GCGATTGGACTGCTTCATTTCTT 60.120 43.478 0.00 0.00 0.00 2.52
137 138 2.421424 GCGATTGGACTGCTTCATTTCT 59.579 45.455 0.00 0.00 0.00 2.52
138 139 2.421424 AGCGATTGGACTGCTTCATTTC 59.579 45.455 0.00 0.00 34.80 2.17
139 140 2.440409 AGCGATTGGACTGCTTCATTT 58.560 42.857 0.00 0.00 34.80 2.32
140 141 2.119801 AGCGATTGGACTGCTTCATT 57.880 45.000 0.00 0.00 34.80 2.57
141 142 2.988010 TAGCGATTGGACTGCTTCAT 57.012 45.000 0.00 0.00 40.06 2.57
142 143 2.988010 ATAGCGATTGGACTGCTTCA 57.012 45.000 0.00 0.00 40.06 3.02
143 144 3.198068 TGAATAGCGATTGGACTGCTTC 58.802 45.455 0.00 0.00 40.06 3.86
144 145 3.266510 TGAATAGCGATTGGACTGCTT 57.733 42.857 0.00 0.00 40.06 3.91
145 146 2.988010 TGAATAGCGATTGGACTGCT 57.012 45.000 0.00 0.00 42.58 4.24
146 147 3.186001 CAGATGAATAGCGATTGGACTGC 59.814 47.826 0.00 0.00 0.00 4.40
147 148 3.744942 CCAGATGAATAGCGATTGGACTG 59.255 47.826 0.00 3.65 0.00 3.51
148 149 3.643320 TCCAGATGAATAGCGATTGGACT 59.357 43.478 0.00 0.00 0.00 3.85
149 150 3.995199 TCCAGATGAATAGCGATTGGAC 58.005 45.455 0.00 0.00 0.00 4.02
150 151 4.687901 TTCCAGATGAATAGCGATTGGA 57.312 40.909 0.00 0.00 0.00 3.53
151 152 5.240183 ACAATTCCAGATGAATAGCGATTGG 59.760 40.000 0.00 0.00 42.97 3.16
152 153 6.204301 AGACAATTCCAGATGAATAGCGATTG 59.796 38.462 0.00 0.00 42.97 2.67
153 154 6.294473 AGACAATTCCAGATGAATAGCGATT 58.706 36.000 0.00 0.00 42.97 3.34
154 155 5.862845 AGACAATTCCAGATGAATAGCGAT 58.137 37.500 0.00 0.00 42.97 4.58
155 156 5.163416 TGAGACAATTCCAGATGAATAGCGA 60.163 40.000 0.00 0.00 42.97 4.93
156 157 5.052481 TGAGACAATTCCAGATGAATAGCG 58.948 41.667 0.00 0.00 42.97 4.26
157 158 6.765036 TCTTGAGACAATTCCAGATGAATAGC 59.235 38.462 0.00 0.00 42.97 2.97
158 159 8.728337 TTCTTGAGACAATTCCAGATGAATAG 57.272 34.615 0.00 0.00 42.97 1.73
159 160 9.690913 ATTTCTTGAGACAATTCCAGATGAATA 57.309 29.630 0.00 0.00 42.97 1.75
160 161 8.591114 ATTTCTTGAGACAATTCCAGATGAAT 57.409 30.769 0.00 0.00 45.75 2.57
161 162 8.413309 AATTTCTTGAGACAATTCCAGATGAA 57.587 30.769 0.00 0.00 37.38 2.57
162 163 9.519191 TTAATTTCTTGAGACAATTCCAGATGA 57.481 29.630 0.00 0.00 0.00 2.92
163 164 9.784680 CTTAATTTCTTGAGACAATTCCAGATG 57.215 33.333 0.00 0.00 0.00 2.90
164 165 8.465201 GCTTAATTTCTTGAGACAATTCCAGAT 58.535 33.333 0.00 0.00 0.00 2.90
165 166 7.448161 TGCTTAATTTCTTGAGACAATTCCAGA 59.552 33.333 0.00 0.00 0.00 3.86
166 167 7.596494 TGCTTAATTTCTTGAGACAATTCCAG 58.404 34.615 0.00 5.10 0.00 3.86
167 168 7.448161 TCTGCTTAATTTCTTGAGACAATTCCA 59.552 33.333 0.00 0.00 0.00 3.53
168 169 7.752686 GTCTGCTTAATTTCTTGAGACAATTCC 59.247 37.037 0.00 0.00 0.00 3.01
169 170 7.752686 GGTCTGCTTAATTTCTTGAGACAATTC 59.247 37.037 0.00 0.00 31.84 2.17
170 171 7.231317 TGGTCTGCTTAATTTCTTGAGACAATT 59.769 33.333 0.00 6.48 31.84 2.32
171 172 6.716628 TGGTCTGCTTAATTTCTTGAGACAAT 59.283 34.615 0.00 0.00 31.84 2.71
172 173 6.061441 TGGTCTGCTTAATTTCTTGAGACAA 58.939 36.000 0.00 0.00 31.84 3.18
173 174 5.620206 TGGTCTGCTTAATTTCTTGAGACA 58.380 37.500 0.00 0.00 31.84 3.41
174 175 5.934625 TCTGGTCTGCTTAATTTCTTGAGAC 59.065 40.000 0.00 0.00 0.00 3.36
175 176 6.114187 TCTGGTCTGCTTAATTTCTTGAGA 57.886 37.500 0.00 0.00 0.00 3.27
176 177 6.652481 TCTTCTGGTCTGCTTAATTTCTTGAG 59.348 38.462 0.00 0.00 0.00 3.02
177 178 6.533730 TCTTCTGGTCTGCTTAATTTCTTGA 58.466 36.000 0.00 0.00 0.00 3.02
178 179 6.808008 TCTTCTGGTCTGCTTAATTTCTTG 57.192 37.500 0.00 0.00 0.00 3.02
179 180 9.520515 TTATTCTTCTGGTCTGCTTAATTTCTT 57.479 29.630 0.00 0.00 0.00 2.52
180 181 9.171877 CTTATTCTTCTGGTCTGCTTAATTTCT 57.828 33.333 0.00 0.00 0.00 2.52
181 182 8.951243 ACTTATTCTTCTGGTCTGCTTAATTTC 58.049 33.333 0.00 0.00 0.00 2.17
182 183 8.870075 ACTTATTCTTCTGGTCTGCTTAATTT 57.130 30.769 0.00 0.00 0.00 1.82
183 184 9.959721 TTACTTATTCTTCTGGTCTGCTTAATT 57.040 29.630 0.00 0.00 0.00 1.40
185 186 9.601217 GATTACTTATTCTTCTGGTCTGCTTAA 57.399 33.333 0.00 0.00 0.00 1.85
186 187 8.982723 AGATTACTTATTCTTCTGGTCTGCTTA 58.017 33.333 0.00 0.00 0.00 3.09
187 188 7.856415 AGATTACTTATTCTTCTGGTCTGCTT 58.144 34.615 0.00 0.00 0.00 3.91
188 189 7.430760 AGATTACTTATTCTTCTGGTCTGCT 57.569 36.000 0.00 0.00 0.00 4.24
189 190 6.419413 CGAGATTACTTATTCTTCTGGTCTGC 59.581 42.308 0.00 0.00 0.00 4.26
190 191 6.419413 GCGAGATTACTTATTCTTCTGGTCTG 59.581 42.308 0.00 0.00 0.00 3.51
191 192 6.096987 TGCGAGATTACTTATTCTTCTGGTCT 59.903 38.462 0.00 0.00 0.00 3.85
192 193 6.199342 GTGCGAGATTACTTATTCTTCTGGTC 59.801 42.308 0.00 0.00 0.00 4.02
193 194 6.043411 GTGCGAGATTACTTATTCTTCTGGT 58.957 40.000 0.00 0.00 0.00 4.00
194 195 6.042777 TGTGCGAGATTACTTATTCTTCTGG 58.957 40.000 0.00 0.00 0.00 3.86
195 196 7.525688 TTGTGCGAGATTACTTATTCTTCTG 57.474 36.000 0.00 0.00 0.00 3.02
196 197 7.819900 AGTTTGTGCGAGATTACTTATTCTTCT 59.180 33.333 0.00 0.00 0.00 2.85
197 198 7.965045 AGTTTGTGCGAGATTACTTATTCTTC 58.035 34.615 0.00 0.00 0.00 2.87
198 199 7.907214 AGTTTGTGCGAGATTACTTATTCTT 57.093 32.000 0.00 0.00 0.00 2.52
199 200 7.907214 AAGTTTGTGCGAGATTACTTATTCT 57.093 32.000 0.00 0.00 0.00 2.40
203 204 9.431887 AGAATTAAGTTTGTGCGAGATTACTTA 57.568 29.630 0.00 0.00 0.00 2.24
204 205 8.230486 CAGAATTAAGTTTGTGCGAGATTACTT 58.770 33.333 0.00 0.00 0.00 2.24
205 206 7.148407 CCAGAATTAAGTTTGTGCGAGATTACT 60.148 37.037 0.00 0.00 0.00 2.24
206 207 6.961554 CCAGAATTAAGTTTGTGCGAGATTAC 59.038 38.462 0.00 0.00 0.00 1.89
207 208 6.403200 GCCAGAATTAAGTTTGTGCGAGATTA 60.403 38.462 0.00 0.00 0.00 1.75
208 209 5.619981 GCCAGAATTAAGTTTGTGCGAGATT 60.620 40.000 0.00 0.00 0.00 2.40
209 210 4.142600 GCCAGAATTAAGTTTGTGCGAGAT 60.143 41.667 0.00 0.00 0.00 2.75
210 211 3.188460 GCCAGAATTAAGTTTGTGCGAGA 59.812 43.478 0.00 0.00 0.00 4.04
211 212 3.058293 TGCCAGAATTAAGTTTGTGCGAG 60.058 43.478 0.00 0.00 0.00 5.03
212 213 2.881513 TGCCAGAATTAAGTTTGTGCGA 59.118 40.909 0.00 0.00 0.00 5.10
213 214 3.281341 TGCCAGAATTAAGTTTGTGCG 57.719 42.857 0.00 0.00 0.00 5.34
214 215 5.695816 TGAAATGCCAGAATTAAGTTTGTGC 59.304 36.000 0.00 0.00 0.00 4.57
215 216 6.925165 ACTGAAATGCCAGAATTAAGTTTGTG 59.075 34.615 0.00 0.00 37.59 3.33
216 217 7.054491 ACTGAAATGCCAGAATTAAGTTTGT 57.946 32.000 0.00 0.00 37.59 2.83
217 218 9.474920 TTTACTGAAATGCCAGAATTAAGTTTG 57.525 29.630 0.00 0.00 37.59 2.93
223 224 9.801873 GCTAATTTTACTGAAATGCCAGAATTA 57.198 29.630 0.00 0.00 37.98 1.40
224 225 8.534496 AGCTAATTTTACTGAAATGCCAGAATT 58.466 29.630 0.00 0.00 37.98 2.17
225 226 8.071177 AGCTAATTTTACTGAAATGCCAGAAT 57.929 30.769 0.00 0.00 37.98 2.40
226 227 7.466746 AGCTAATTTTACTGAAATGCCAGAA 57.533 32.000 0.00 0.00 37.98 3.02
227 228 7.315142 CAAGCTAATTTTACTGAAATGCCAGA 58.685 34.615 0.00 0.00 37.98 3.86
228 229 6.035327 GCAAGCTAATTTTACTGAAATGCCAG 59.965 38.462 0.00 0.00 37.98 4.85
229 230 5.868801 GCAAGCTAATTTTACTGAAATGCCA 59.131 36.000 0.00 0.00 37.98 4.92
230 231 5.291858 GGCAAGCTAATTTTACTGAAATGCC 59.708 40.000 0.92 0.92 38.20 4.40
231 232 6.035327 CAGGCAAGCTAATTTTACTGAAATGC 59.965 38.462 0.00 0.00 37.98 3.56
232 233 7.315142 TCAGGCAAGCTAATTTTACTGAAATG 58.685 34.615 0.00 0.00 37.98 2.32
233 234 7.466746 TCAGGCAAGCTAATTTTACTGAAAT 57.533 32.000 0.00 0.00 39.63 2.17
234 235 6.892658 TCAGGCAAGCTAATTTTACTGAAA 57.107 33.333 0.00 0.00 31.51 2.69
235 236 6.264292 TGTTCAGGCAAGCTAATTTTACTGAA 59.736 34.615 0.00 0.00 40.26 3.02
236 237 5.767665 TGTTCAGGCAAGCTAATTTTACTGA 59.232 36.000 0.00 0.00 32.47 3.41
237 238 6.012658 TGTTCAGGCAAGCTAATTTTACTG 57.987 37.500 0.00 0.00 0.00 2.74
238 239 6.648879 TTGTTCAGGCAAGCTAATTTTACT 57.351 33.333 0.00 0.00 0.00 2.24
239 240 6.934561 CTTGTTCAGGCAAGCTAATTTTAC 57.065 37.500 0.00 0.00 39.26 2.01
250 251 2.687935 GGTTTCAGACTTGTTCAGGCAA 59.312 45.455 0.00 0.00 29.16 4.52
251 252 2.092429 AGGTTTCAGACTTGTTCAGGCA 60.092 45.455 0.00 0.00 29.16 4.75
252 253 2.291741 CAGGTTTCAGACTTGTTCAGGC 59.708 50.000 0.00 0.00 31.17 4.85
253 254 2.880890 CCAGGTTTCAGACTTGTTCAGG 59.119 50.000 0.00 0.00 33.75 3.86
254 255 2.880890 CCCAGGTTTCAGACTTGTTCAG 59.119 50.000 0.00 0.00 33.75 3.02
255 256 2.507886 TCCCAGGTTTCAGACTTGTTCA 59.492 45.455 0.00 0.00 33.75 3.18
256 257 3.142174 CTCCCAGGTTTCAGACTTGTTC 58.858 50.000 0.00 0.00 33.75 3.18
257 258 2.509964 ACTCCCAGGTTTCAGACTTGTT 59.490 45.455 0.00 0.00 33.75 2.83
258 259 2.127708 ACTCCCAGGTTTCAGACTTGT 58.872 47.619 0.00 0.00 33.75 3.16
259 260 2.938956 ACTCCCAGGTTTCAGACTTG 57.061 50.000 0.00 0.00 35.27 3.16
260 261 5.584551 ATTTACTCCCAGGTTTCAGACTT 57.415 39.130 0.00 0.00 0.00 3.01
261 262 5.338463 GCTATTTACTCCCAGGTTTCAGACT 60.338 44.000 0.00 0.00 0.00 3.24
262 263 4.876679 GCTATTTACTCCCAGGTTTCAGAC 59.123 45.833 0.00 0.00 0.00 3.51
263 264 4.534500 TGCTATTTACTCCCAGGTTTCAGA 59.466 41.667 0.00 0.00 0.00 3.27
264 265 4.843728 TGCTATTTACTCCCAGGTTTCAG 58.156 43.478 0.00 0.00 0.00 3.02
265 266 4.919774 TGCTATTTACTCCCAGGTTTCA 57.080 40.909 0.00 0.00 0.00 2.69
266 267 7.875327 TTTATGCTATTTACTCCCAGGTTTC 57.125 36.000 0.00 0.00 0.00 2.78
267 268 7.893833 AGTTTTATGCTATTTACTCCCAGGTTT 59.106 33.333 0.00 0.00 0.00 3.27
268 269 7.410991 AGTTTTATGCTATTTACTCCCAGGTT 58.589 34.615 0.00 0.00 0.00 3.50
269 270 6.970191 AGTTTTATGCTATTTACTCCCAGGT 58.030 36.000 0.00 0.00 0.00 4.00
270 271 7.444487 GGTAGTTTTATGCTATTTACTCCCAGG 59.556 40.741 0.00 0.00 0.00 4.45
683 685 1.037493 CGTATCCCCGTCATTCCAGA 58.963 55.000 0.00 0.00 0.00 3.86
975 977 7.776107 TGAACACATCAACAAAATCACCTTAA 58.224 30.769 0.00 0.00 34.30 1.85
1051 1053 1.986882 CAGGTGGGTTCAGAAAGCTT 58.013 50.000 0.00 0.00 33.34 3.74
1118 1120 3.487120 AGAAACGCCTTCCAGTTAAGT 57.513 42.857 0.00 0.00 34.21 2.24
1370 1372 6.368791 TGCTTGTACAAGTACATTCACAGATC 59.631 38.462 30.90 13.41 44.54 2.75
1614 1618 1.077716 GGTACATGTCCCACAGCCC 60.078 63.158 0.00 0.00 0.00 5.19
1702 1706 5.888105 ACTCAATGCACAGCTTATCATTTC 58.112 37.500 0.00 0.00 0.00 2.17
3044 3050 7.880160 ATGAAACCTATGTATTTGCTTGCTA 57.120 32.000 0.00 0.00 0.00 3.49


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.